Globally, tuberculosis (TB) is the most widespread infectious disease. One third of the world's population (2 billion people) are infected with M. tuberculosis and 5-10% of these suffer active disease, leading to nearly 3 million deaths annually. Although, in the long-term, vaccination is the only way to eliminate tuberculosis, especially in developing countries where lengthy combination drug therapy is problematical, this does not address the need of the 2 billion individuals who are infected right now nor of the alarmingly growing number of patients in developed countries who are suffering from multidrug-resistant (MDR) TB, which is essentially refractory to drug therapy (Espinal et al., N. Engl. J. Med. 344:1294-1303 (2001)). A special concern is the link between AIDS and TB. Thirty-one % of TB cases in Africa and 26% of those in the USA are associated with HIV infection and the death of 11% of all HIV patients is caused by TB (Corbett et al., Arch. Intern. Med. 163: 1009-1021 (2003)). The mainline anti-tuberculosis drugs isoniacid, rifampin, pyrazinamide, ethambutol, and, secondarily, streptomycin thus need be supplemented by additional drugs against new targets, until those, too, succumb to resistance mechanisms. It is therefore important to keep developing an armamentarium of drugs against a wide range of targets to use in combination with established drugs and replace these when they begin to fail. In addition, the ability of M. tuberculosis to persist in a patient for decades in a state refractory to most known antibacterial agents puts a great premium on the discovery of new drugs capable of targeting the persistent state. Another context in which a new type of anti-mycobacterial drugs would play an important role is in response to bioterrorist attacks that may involve M. tuberculosis. In such a situation, it may be desirable to treat large populations prophylactically to avoid the establishment of infections, the treatment of which would require a long course of costly multidrug therapy.
The search for new anti-tuberculosis drugs aimed at new targets therefore deserves to be given high priority. Effective cure of MDR TB requires long-term treatment with anti-TB drugs and that in the event of a bioterrorist attack, large populations must be treated prophylactically with a suitable antibiotic. If the antibiotic to be used in these situations were a broad-spectrum drug, it would not only affect a significant fraction of the subject's normal bacterial flora but could stimulate the emergence of resistance among other pathogens carried by the treated population. These problems would not arise with a drug targeted specifically against M. tuberculosis. 
DnaB is a DNA helicase that functions in the initiation of lagging-strand DNA synthesis (Arai and Kornberg, Proc. Natl. Acad. Sci. USA 76: 4308-4312 (1979)) as a component of the primosome (Saluja and Godson, J. Bacteriol. 177: 1104-1111 (1995)). Specifically, it unwinds the DNA duplex ahead of the replication fork and recruits the DnaG primase to the primosome. The essential role of E. coli DnaB in DNA replication is indicated by the existence of temperature-sensitive dnaB mutants (Kogama, T., J. Mol. Biol. 103: 191-197 (1976)). The functional form of the DnaB protein is a hexamer which interacts directly with 2-3 molecules of the DnaG primase (Bird et al., Biochemistry 39: 171-182 (2000)). In the light of the complex protein-protein interactions in which DnaB participates, which may also include the products of the dnaA, dnaC, and dnaX genes, it is quite unlikely that the 465-residue DnaB helicase can function without the excision of the 415-residue intein.
As in enteric bacteria, the M. tuberculosis RecA protein initiates the SOS response to DNA damage by polymerizing to filaments at the site of DNA lesions (Movahedzadeh et al., J. Bacteriol. 179: 3509-3518 (1997)). However, a major difference between M. tuberculosis and other bacteria in the induction of the SOS response is that the M. tuberculosis RecA protein is synthesized in an inactive form, which has to undergo protein splicing before it can assume its role in the initiation of DNA repair. It should be noted that RecA is not essential for bacterial growth except under conditions of excessive DNA damage. Since M. tuberculosis is an intracellular pathogen, the repair of DNA damage inflicted by the reactive oxygen and nitrogen species produced by macrophages must play an important role in its survival in the infected host. However, recA mutants of M. bovis BCG, a non-virulent mycobacterial strain but highly susceptible to killing by DNA damaging agents, were not compromised in terms of survival in a nude mouse model, but, when studied in an in vitro model for persistence, had a greatly enhanced sensitivity to metronidazole (Sander et al., Inf. Immun. 69: 3562-3568 (2001)). On the other hand, recent work has suggested an important role of RecA on in vivo survival and the emergence of drug resistant mycobacteria. One of the enzymes, which is induced by the SOS response to DNA damage (Davis et al., J. Bacteriol. 184: 3287-3295 (2002)) and whose induction absolutely requires functional RecA (Rand et al., Mol. Microbiol. 50: 1031-1041 (2003)), is an error-prone DNA polymerase, DnaE2 (Boshoff et al., Cell 113: 183-193 (2003)). In Mycobacterium smegmatis, disruption of either dnaE2 or recA reduced the number of UV-induced RifR mutations 10- to 25 fold, respectively, to nearly background levels. In M. tuberculosis, only the effect of dnaE2 disruption was examined, which essentially prevented any DNA damage induced RifR mutations and, when tested in an infected mouse model, almost doubled the medium survival time and reduced lung CFU counts nine month post-infection 10-fold (Boshoff et al., Cell 113:183-193 (2003)). DnaE2 and, by extension, RecA, which is essential for DnaE2 induction, thus appear to be important players in the emergence of drug-resistance mutations and in the longterm survival of M. tuberculosis in the infected host.
Protein splicing is a form of post-translational processing that consists of the excision of an intervening polypeptide sequence, the intein, from a protein, accompanied by the concomitant joining of the flanking polypeptide sequences, the exteins, by a peptide bond (FIG. 1). It proceeds by a series of four reactions that are catalyzed entirely by the intein and require no cofactors or accessory proteins (Paulus, H., Annu. Rev. Biochem. 69: 447-496 (2000)). About 200 inteins are known, distributed in unicellular representatives of eukaryotes, archaea, and bacteria (Perler, F. B., Nucl. Acids Res. 30: 383-384 (2002)). The fact that protein splicing does not occur in higher eukaryotes and has a limited distribution among eubacteria, with Mycobacterium as the only pathogenic representative, makes it a very attractive antimycobacterial target.
M. tuberculosis harbors three inteins, which interrupt the DnaB, RecA, and SufB (Rv1461) proteins. As discussed in the next section, the DnaB and RecA proteins play important roles in DNA replication and repair, respectively, whereas SufB is a component of the Fe—S cluster assembly and repair SUF machinery (Huet, G., Daffe, M., and Saves, I. J Bacteriol 187: 6137-6146 (2005)) and is essential for growth (Sassetti, C. M., Boyd, D. H., and Rubin, E. J. Mol. Microbiol 48: 77-84 (2003)). We have focused our attention on the DnaB and RecA inteins, whose protein splicing domains, compared in FIG. 2, show 29% amino acid identity and 44% similarity, not only in the conserved protein splicing motifs but in other regions, suggesting a close evolutionary relationship. The high degree of similarity of these inteins, as well as the fact that even relatively unrelated inteins have almost identical 3-D structures (e.g., Paulus, Annu. Rev. Biochem. 69:447-496 (2000)), makes it quite likely that substances can be found which are inhibitors of protein splicing catalyzed by both of these inteins. Although we are not specifically focusing on the study of the SufB (Rv1461) intein, its protein splicing domain has 17% identity and 31% similarity to the that of the DnaB intein, suggesting that its structure is similar to the structure of the DnaB and RecA inteins and that all three inteins may be susceptible to the same inhibitors.
Protein splicing inhibitors that inhibit the function of both the DnaB and the RecA inteins hold several important advantages as anti-TB drugs. First, the inhibition of two separate targets, DNA replication (DnaB) and DNA repair (RecA) would produce synergistic effects, leaving more chance of success against infection. Secondly, the inhibitors by design would not interact with DnaB and RecA directly and resistance could therefore not arise from mutations in the catalytic domains of these proteins but only from mutations in the intein. It is known that the majority of intein mutations leads to uncoupling of the protein splicing pathway (Chong et al., J. Biol. Chem. 273: 10567-10577 (1998)), which would result in a reduction of protein splicing activity instead of fostering resistance. Additionally, inhibition of DnaB would directly inhibit growth and simultaneous inhibition of RecA would prevent induction of error-prone DNA repair. Since error-prone DNA repair contributes to persistence and most mutations to drug-resistance, inhibition of the same would suppress the emergence and growth of bacterial strains with inhibitor-resistant DnaB and RecA inteins. Finally, because higher eukaryotes, pathogens other than Mycobacterium, and bacteria normally associated with humans do not bear inteins, protein splicing inhibitors would therefore be narrow spectrum antibiotics specific for Mycobacterium. Resultingly, such inhibitors would be expected to have no major side effects.